#!/bin/bash

ptraj_file="tmp.ptraj"
OUT="50ns_noWAT_500frames"

REF="1XCK_chainA_sol.inpcrd"

PRMTOP="../../1XCK_apo_noWAT.prmtop"

TRAJIN[1]="../traj/50ns_5000frames_noWAT.nc"


MASK[1]=":1-524,5765-6288,6289-6812"
MASK[2]=":525-1048,5241-5764,5765-6288"
MASK[3]=":1049-1572,4717-5240,5241-5764"
MASK[4]=":1573-2096,4193-4716,4717-5240"
MASK[5]=":2097-2620,3669-4192,4193-4716"
MASK[6]=":2621-3144,3669-4192,6813-7336"
MASK[7]=":3145-3668,6289-6812,6813-7336"



rm ${ptraj_file}

for index in 1;
do
        echo 'trajin '${DIR[index]}${TRAJIN[1]} 1 5000 10 >> ${ptraj_file}

        echo "strip '* & !"${MASK[index]}"'" >> ${ptraj_file}
        #echo "strip @H*" >> ${ptraj_file}

	#echo 'rms first mass :8-27,52-58-133,416-456,496-514@N,CA,C' >> $ptraj_file
	echo 'rms first mass @N,CA,C' >> $ptraj_file
        echo 'trajout '${OUT}"_chain_"${index}".dcd charmm" >> ${ptraj_file}

        ptraj ${PRMTOP} ${ptraj_file}

        rm ${ptraj_file}
done